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- PDB-7r4b: The Bacillus pumilus chorismate mutase -

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Basic information

Entry
Database: PDB / ID: 7r4b
TitleThe Bacillus pumilus chorismate mutase
ComponentsChorismate mutase AroH
KeywordsISOMERASE / chorismate / prephenic / mutase
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
Similarity search - Function
Chorismate mutase, AroH class / Chorismate mutase type I / Chorismate mutase domain profile. / RutC-like superfamily
Similarity search - Domain/homology
Chorismate mutase AroH
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLund, B.A.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway262695 Norway
Research Council of Norway274858 Norway
CitationJournal: To Be Published
Title: The Bacillus pumilus chorismate mutase
Authors: Wilkins, R. / Lund, B.A. / Isaksen, G.V. / Brandsdal, B.O. / Aqvist, J.
History
DepositionFeb 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chorismate mutase AroH
B: Chorismate mutase AroH
C: Chorismate mutase AroH
D: Chorismate mutase AroH
E: Chorismate mutase AroH
F: Chorismate mutase AroH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3527
Polymers92,2896
Non-polymers621
Water14,772820
1
B: Chorismate mutase AroH
C: Chorismate mutase AroH

A: Chorismate mutase AroH


Theoretical massNumber of molelcules
Total (without water)46,1453
Polymers46,1453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area6610 Å2
ΔGint-36 kcal/mol
Surface area14740 Å2
2
D: Chorismate mutase AroH
E: Chorismate mutase AroH
F: Chorismate mutase AroH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2074
Polymers46,1453
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-35 kcal/mol
Surface area15120 Å2
Unit cell
Length a, b, c (Å)49.898, 94.864, 77.305
Angle α, β, γ (deg.)90.000, 107.487, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chorismate mutase AroH


Mass: 15381.579 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: SAFR-032 / Gene: BPUM_2000 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8FEK3, chorismate mutase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 820 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5 25% PEG 1500 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→24.58 Å / Num. obs: 227592 / % possible obs: 78.3 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 12.99
Reflection shellResolution: 1.1→1.139 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 6262 / CC1/2: 0.244 / Rpim(I) all: 0.9 / % possible all: 22.6

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
XDS0.86data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zo8

3zo8


Resolution: 1.1→24.58 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.042
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1965 1904 0.878 %
Rwork0.1823 215057 -
all0.182 --
obs-216961 78.227 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.128 Å20 Å20.123 Å2
2--0.241 Å2-0 Å2
3----0.159 Å2
Refinement stepCycle: LAST / Resolution: 1.1→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5678 0 4 820 6502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126009
X-RAY DIFFRACTIONr_bond_other_d0.0540.0165997
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.6448180
X-RAY DIFFRACTIONr_angle_other_deg1.9391.5713610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44222.75320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.536151128
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg5.3831512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2831543
X-RAY DIFFRACTIONr_chiral_restr0.0760.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026784
X-RAY DIFFRACTIONr_gen_planes_other0.0150.021326
X-RAY DIFFRACTIONr_nbd_refined0.2310.21235
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.25847
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23012
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.23469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2760.2585
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1490.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.239
X-RAY DIFFRACTIONr_nbd_other0.2460.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.250
X-RAY DIFFRACTIONr_mcbond_it1.1451.3222973
X-RAY DIFFRACTIONr_mcbond_other1.1531.3212972
X-RAY DIFFRACTIONr_mcangle_it1.761.9783746
X-RAY DIFFRACTIONr_mcangle_other1.7631.983747
X-RAY DIFFRACTIONr_scbond_it2.2781.6863036
X-RAY DIFFRACTIONr_scbond_other2.2821.6863037
X-RAY DIFFRACTIONr_scangle_it3.7012.4064434
X-RAY DIFFRACTIONr_scangle_other3.7012.4074435
X-RAY DIFFRACTIONr_lrange_it5.65218.4816986
X-RAY DIFFRACTIONr_lrange_other5.25717.5416749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.1280.481330.4313697X-RAY DIFFRACTION18.1951
1.128-1.1590.365690.3727550X-RAY DIFFRACTION38.2192
1.159-1.1930.372920.34910261X-RAY DIFFRACTION53.2452
1.193-1.2290.3231180.32513938X-RAY DIFFRACTION74.7342
1.229-1.270.2951320.28914785X-RAY DIFFRACTION81.6564
1.27-1.3140.2791360.26315199X-RAY DIFFRACTION86.5211
1.314-1.3640.2551390.24514940X-RAY DIFFRACTION88.7209
1.364-1.4190.2471280.23514523X-RAY DIFFRACTION89.1614
1.419-1.4830.2421210.21813696X-RAY DIFFRACTION87.5436
1.483-1.5550.181170.19713945X-RAY DIFFRACTION93.4538
1.555-1.6390.2451190.18513412X-RAY DIFFRACTION94.4836
1.639-1.7380.1761130.17912749X-RAY DIFFRACTION94.8805
1.738-1.8580.1991060.16612034X-RAY DIFFRACTION95.3129
1.858-2.0070.153930.15510516X-RAY DIFFRACTION89.2863
2.007-2.1980.166880.15110556X-RAY DIFFRACTION97.419
2.198-2.4580.169890.159556X-RAY DIFFRACTION97.5918
2.458-2.8370.183720.1518399X-RAY DIFFRACTION97.1445
2.837-3.4740.174640.1567005X-RAY DIFFRACTION95.3466
3.474-4.9070.14480.1365244X-RAY DIFFRACTION91.6681
4.907-24.580.189270.1753052X-RAY DIFFRACTION96.2188

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